vertesy / ggexpress Goto Github PK

function(vec, ext = "pdf", plot = TRUE, save = TRUE, mdlink = TRUE
                     , hline = F, filtercol = 1
                     , xlab.angle = 90, xlab = F
                     , w = 5, h = w, ...) {
  plotname <- as.character(substitute(vec))
...

 qqqParsePlotname(vec, suffix)

qbarplot <- function(vec, ext = "pdf", plot = TRUE
                     , suffix = NULL
                     , plotname = qqqParsePlotname(vec, suffix)
                     # , title = F
                     , save = TRUE, mdlink = FALSE
                     , hline = F, filtercol = 1
                     , palette_use = 'jco', col = as.character(1:3)[1]
                     , xlab.angle = 90, xlab = F
                     , logY = F
                     , label = NULL
                     , max.names = 50
                     , limitsize = FALSE
                     , w = qqqAxisLength(vec), h = 5, ...) {

  df[["colour"]] <- if (vline & filtercol != 0) {
    if (filtercol == 1 ) (df$"value" > vline) else if (filtercol == -1 ) (df$"value" < vline)
  } else if (length(col) == length(vec)) {
    as.character(col)
  } else {
    as.character(rep(col, length(vec))[1:length(vec)])
  }

 dev.copy2pdf(
      file = ww.FnP_parser(fname_, "pdf"),
      width = w_,
      height = h_,
      title = ww.ttl_field(fname_)

df <- qqqCovert.named.vec2tbl(namedVec = vec, strip.too.many.names = F)
 Error in print.default("Vector has", thr, "+ names. Can mess up auto-color legends.") : 
invalid printing digits 50

my_tibble <- tibble(
  Column_1 = c("A", "A", "A", "B", "C", "C"),
  Column_2 = c("X", "Y", "Y", "Z", "X", "Z")
)
freq_table <- my_tibble %>% count(Column_1, Column_2)
qbarplot.df(freq_table)
qbarplot.df(my_tibble)

example_tibble <- tibble(
  ID = rep(c("A", "B", "C"), times = 4),
  Time = rep(1:4, each = 3),
  Value = rnorm(12)
)

qbarplot.df(example_tibble)

> qbarplot.df(example_tibble)
Error in median(as.numeric(df[, y])) : 
  'list' object cannot be coerced to type 'double'

xvec <- c("A"=12, "B"=29); 
qpie(vec = xvec)
qpie(vec = xvec, both_pc_and_value = T)

datX = c(A.1 = 15273817120.75, A.2 = 19748042499.75, A.3 = 19015562583.97, A.4 = 19539107256.48, A.5 = 20293595960.89, A.6 = 18401588363.56, A.7 = 18876623322.12, A.8 = 20113344495.41, A.9 = 19759801754.07, A.10 = 19862305126.29, B.1 = 14049263285.29, B.2 = 15310874767.7, B.3 = 13316238905.88, B.4 = 13053793265.22, B.5 = 12451837184.56, B.6 = 15095732257.66, B.7 = 13793883930.1, B.8 = 14145915911.97, B.9 = 14029136875.07, B.10 = 16434420425.09, C.1 = 16634725276.67, C.2 = 17635189764.07, C.3 = 18453442284.71, C.4 = 18140879520.46, C.5 = 19454822015.85, C.6 = 19472830899.79, C.7 = 19187828858.17, C.8 = 19290220121.02, C.9 = 19176960564.72, C.10 = 18101441453.02, D.1 = 16194435630.05, D.2 = 18078756773.13, D.3 = 17579176095.34, D.4 = 16857272399.08, D.5 = 17902504889.1, D.6 = 17689611098.42, D.7 = 17892178766.36, D.8 = 17819751385.79, D.9 = 16896316453.25, D.10 = 17843222873.72, E.1 = 19266947287.15, E.2 = 19102158394.34, E.3 = 18135419322.44, E.4 = 18720949164.04, E.5 = 19172455475.47, E.6 = 17089109522.67, E.7 = 19203272180.69, E.8 = 19543017029.51, E.9 = 17488648870.63, E.10 = 18433494529.85, F.1 = 16373913388.65, F.2 = 17247845170.57, F.3 = 17309605641.54, F.4 = 16811631542.41, F.5 = 17734956810.56, F.6 = 17629744406.91, F.7 = 17552351271.36, F.8 = 17887451319.71, F.9 = 17912108211.29, F.10 = 18339746215.46, G.1 = 13032074439.62, G.2 = 13268056651.77, G.3 = 12768107933.15, G.4 = 11318557947.43, G.5 = 13112409433.13, G.6 = 12970230567.49, G.7 = 12447675596.99, G.8 = 11066276951.24, G.9 = 11787443223.6, G.10 = 14026544366.27, H.1 = 21877575254.63, H.2 = 24743269000.6, H.3 = 23873349116.16, H.4 = 25843702092.69, H.5 = 24832172670.89, H.6 = 26174812828.44, H.7 = 25820908847.56, H.8 = 24123991349.34, H.9 = 26286380503.78, H.10 = 1765156596.59, I.1 = 22004381857.62, I.2 = 19878260460.73, I.3 = 22679932183.01, I.4 = 21000909188.35, I.5 = 23336329575.16, I.6 = 23889551306.53, I.7 = 23551824810.83, I.8 = 21266124403.33, I.9 = 23571944492.02, I.10 = 1460005444.33, J.1 = 20887643832.89, J.2 = 22482078231.65, J.3 = 22819414495.48, J.4 = 24019122823.56, J.5 = 23243883898.4, J.6 = 22590511082.91, J.7 = 23752435598.41, J.8 = 22748121492.62, J.9 = 19315053455.04, J.10 = 1259362111.49, K.1 = 23540019932.29, K.2 = 24775818787.02, K.3 = 20386348553.98, K.4 = 25039316068.69, K.5 = 20917657564.64, K.6 = 20289950682.21, K.7 = 25211705926.88, K.8 = 23043947654.76, K.9 = 24970635486.15, K.10 = 1291511169.53, L.1 = 16237995863.11, L.2 = 20137547157.36, L.3 = 9704396265.18, L.4 = 19494896522.97, L.5 = 20357174248.84, L.6 = 20501902989.71, L.7 = 20507997756.31, L.8 = 20224579660.29, L.9 = 20472644107.52, L.10 = 1429814856.84, M.1 = 17093855098.68, M.2 = 22708468267.65, M.3 = 17112070009.12, M.4 = 19340725263.25, M.5 = 19109316557.26, M.6 = 9152375748.16, M.7 = 11789601377.25, M.8 = 10044131051.83, M.9 = 15977978843.56, M.10 = 12057889990.24, N.1 = 14309581287.03, N.2 = 16252468032.82, N.3 = 6968983806.91, N.4 = 13877044327.23, N.5 = 14220131960.2, N.6 = 9820674445.55, N.7 = 13536157372.82, N.8 = 13098031419.04, N.9 = 12511073551.64, N.10 = 12412045225.81, O.1 = 19985770044.07, O.2 = 18697038222.58, O.3 = 17542698389.18, O.4 = 17771104040.35, O.5 = 16599569895.31, O.6 = 20143989602.36, O.7 = 14641182791.99, O.8 = 15069290758.51, O.9 = 13971684113.31, O.10 = 7719658618.26, P.1 = 15105992372.21, P.2 = 15618543642.25, P.3 = 16519924399.5, P.4 = 18341317197.64, P.5 = 19920739997.97, P.6 = 14681411340.91, P.7 = 17025792187.53, P.8 = 13852606495.48, P.9 = 15357227597.44, P.10 = 15597400318.06, Q.1 = 18073761261.9, Q.2 = 15269826705.96, Q.3 = 19992603326.46, Q.4 = 13523915647.89, Q.5 = 19302407210, Q.6 = 13750064354.38, Q.7 = 13816139874.54, Q.8 = 17878540640.13, Q.9 = 21338075539.85, Q.10 = 11137639240.29)

qbarplot(datX)

refilter.assigned.to.cells.X
   0    1    2    3    4    5    6    7    8    9   10   11   12   13 
1534 1011  328  157   78   51   30   15   20   18    4    3    5    2 
  14   15   16   17   18   19   25   28   29   33   34 
   2    2    1    2    2    1    1    1    1    1    1 

Error in seq.default(min, max, by = by) : 'from' must be a finite number

  qbarplot(Nr.of.UVIs.per.cell, label = Nr.of.UVIs.per.cell, palette_use = "aaas"
           , suffix = NewObj_names[i]
...
)

NOT LOGGED: Log path and filename is not defined in path_of_report
Error in (MarkdownHelpers::llogit())(paste0("![", file_name, "]", "(",  : 
  attempt to apply non-function

 shistogram(Total.Starter.Expr.per.cell)
[1] 11
[1] 2222
[1] "/Users/abel.vertesy/Dropbox/Abel.IMBA/AnalysisD/Abel/CON/p2.v2020.11.premRNA./RabV.Filter/Total.Starter.Expr.per.cell.hist.pdf"
[1] 22222

shistogram <-  function(vec, ext = "pdf", xlab = F, vline = F, plot = TRUE, ...) {
  plotname <- as.character(substitute(vec))
  if(isFALSE(xlab)) xlab = plotname
  df <- qqCovert.hist(namedVec = vec)
  p <- gghistogram(data = df, x = "value"
                   , title = plotname, xlab = xlab
                   , add = "median"
                   , color = "names", fill = "names"
                   , palette = 'jco', ...
  ) +
    if (length(unique(df$"names")) == 1) theme(legend.position = "none")
  if (vline) p <- p + geom_vline(xintercept = vline)
  fname = kpp(plotname, "hist",  ext)
  print(11)
  qqSave(ggobj = p, title = plotname, fname = fname)
  print(1121)
  # if (plot) p
}

# ------------------------------------------------------------------------------------------------
qqSave <- function(ggobj, ext =c("png", "pdf")[2], w =4, h = w
                   , title = F, fname = F, ...) {
  if(isFALSE(title)) title = substitute(ggobj)
  if(isFALSE(fname)) fname <- kpp(title, ext)
  print(2222)
  print(paste0(getwd(),"/", fname))
  print(22222)
  # cowplot::save_plot(plot = ggobj, filename = fname, base_height = w, base_width = h)
  ggsave2(plot = ggobj, filename = fname, height = w, width = h)
}

Total.Starter.Expr.per.cell <- colSums(EXPR.XXgenes[genes.primary.cells, ])
shistogram(Total.Starter.Expr.per.cell)

 color = "colour", fill = "colour", 

qqqParsePlotname <- function(string = "sadsad", suffix_tag= NULL) { # parse plot name from variable name and suffix
  nm <- make.names((substitute(string)))
  if (!is.null(suffix_tag) & !isFALSE(suffix_tag)) nm <- Stringendo::kpp(nm, suffix_tag)
  print(11)
  print(nm)
  
  return(nm)
}


qpie <- function(vec, ext = "pdf", plot = TRUE, save = TRUE, mdlink = FALSE
                 , suffix = NULL
                 , plotname = FixPath() kpp(substitute(vec), suffix)
                 , LegendSide = T, LegendTitle = as.character(substitute(vec)), NoLegend = F
                 , pcdigits = 2, NamedSlices =F
                 , custom.order = F
                 # , custom.margin = F
                 , palette_use = 'jco'
                 , max.names = 50
                 , w = 5, h = w, ...) {
  
  df <- qqqCovert.named.vec2tbl(namedVec = vec, thr = max.names)
  nrCategories.DFcol1 <- length(unique(df[,1])); stopif( nrCategories.DFcol1 > 100)
  
  pcX <- df$"value" / sum(df$"value")
  labs <- paste(100 * signif (pcX, pcdigits), "%", sep = "")
  if (NamedSlices) labs <- paste(df$names, "\n", labs)
  print(df)
  if (custom.order != F) df$'names' <- factor(df$'names', levels = custom.order)
  
  p <- ggpubr::ggpie(data = df, x = "value", label = labs
                     , fill = "names", color = "white"
                     , title = plotname
                     , palette = palette_use, ...)
  if (LegendSide) p <- ggpubr::ggpar(p, legend = "right", legend.title = LegendTitle)
  # if (custom.margin) p <- p + theme(plot.margin = unit(custom.margin, "cm"))
  # p <- if (NoLegend) p + NoLegend() else p
  p <- if (NoLegend) p + theme(legend.position = "none", validate = TRUE) else p
  fname = Stringendo::kpp(plotname, suffix, "pie",  ext)
  if (save) qqSave(ggobj = p, title = plotname, fname = fname, ext = ext, w = w, h = h)
  if (mdlink & save) qMarkdownImageLink(fname)
  if (plot) p
}



abc <- 1:3
qpie(abc)

df <- data.frame(
  group = c("Male", "Female", "Children but not teenager"),
  value = c(25, 25, 50))

ggpie(df, "value", label = "group")

ggobj +
    theme(plot.margin = unit(c(1,1,1,1), "cm"))

 Error in grDevices::png(...) : 
  unused arguments (title = ...)

── Conflicts ─────────────────────────────────── ggExpress conflicts ──
x flag.nameiftrue() masks ggExpress::flag.nameiftrue()
x kpp()             masks ggExpress::kpp()

if (!require("pacman")) install.packages("pacman")
pacman::p_load(dplyr, venneuler)
pacman::p_load_current_gh('trinker/textshape', 'thomasp85/ggforce')


x <- matrix(sample(0:4, 80, TRUE, c(.6, .1, .1, .1, .1)), ncol=4)

colnames(x) <- LETTERS[1:4]


euler_dat <- split(as.data.frame(x), c(T, F)) %>%
    setNames( c('dog', 'cat')) %>%
    lapply(function(x){ rownames(x) <- letters[1:10]; x}) %>%
    lapply(function(x){
        y <- venneuler(x)
        data.frame(y$centers, diameters = y$diameters, labels = y$labels, stringsAsFactors = FALSE)
    }) %>%
    textshape::bind_list('animal')

euler_dat %>%
    mutate(r = diameters/2) %>%
    ggplot() +
        geom_circle(aes(x0 = x, y0 = y, r = r, fill=labels), alpha = .5) +
        facet_wrap(~animal) +
        geom_text(aes(x = x, y = y, label = labels)) +
        coord_fixed()